Rodomoc;

The design you suggested implies removing every component on the Pegasos and reimplementing it with another set of chipsets. Apart from connector locations and the layout of the backplane - if you even kept those, I doubt it since you would have to make a lot of room for the CPU, and add far more than the Pegasos had - you would be about as far removed from Pegasos as the Mac Mini is. That is to say, it would not even be worth using the Pegasos as a reference.

You may as well start designing a brand new board from scratch, and if you are putting the CPU on the motherboard, why not just use the MPC8610 or MPC8641D and save yourself some PCB space?